Martin Winterkorn was indicted on four counts of conspiracy and wire fraud, becoming the most senior VW executive to be charged in connection with the scandal.
Winterkorn became the ninth person to face U.S. criminal charges in connection with the scandal.
Five other executives were charged in 2016.
Mr Winterkorn has been accused of conspiring to mislead regulators about the fraudulent emissions testing, defrauding United States customers, and wire fraud, making him the ninth person to be hit with USA criminal charges connected to the "Dieselgate" scandal. The other three counts alleged wire fraud in connection with the scheme.
He allegedly found out of the so-called defeat device installed in the carmaker's cars in 2014, following a study of West Virginia University's Center for Alternative Fuels, Engines, and Emissions.
Volkswagen executives were accused of deliberately misleading USA regulators by installing a "defeat device" in 11m vehicles worldwide, embedded software which allowed vehicles to recognise when the were being tested in laboratory conditions and reduce emissions levels accordingly.
The meeting provided a "clear picture" of how the company was deceiving USA regulators about software used to rig emissions tests of Volkswagen diesel vehicles, it said.
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In May, a VW Executive sent a memo to Winterkorn explaining the situation which stated, "a thorough explanation for the dramatic increase in NOx emissions can not be given to the authorities".
The U.S. government believes Winterkorn is in Germany, so it's unlikely he'll ever see a U.S. courtroom or jail. Documents later surfaced tying several executives to statements imploring colleagues to "come up with the story please!" when regulators started asking questions.
In July 2015, when the United States threatened not to re-certify Volkswagen diesels because their emissions numbers were so off, Winterkorn asked his employees for a briefing on the situation. Volkswagen has also been forced to buy back over 5 lakh running vehicles from owners, which have now been stored in lots around the country. It was internally referred to as the "damage table meeting".
Mr Winterkorn, who resigned from the company as a storm erupted over the company's behaviour in September 2015, has always maintained he knew nothing about software created to cheat lab emission tests.
The charges stem from the VW Group diesel emissions scandal that broke in 2015.
However, the whole charade fell apart at that CARB meeting as a Volkswagen employee in "direct contravention of the instructions from his superiors" revealed the company's 2.0-liter TDI engines were using defeat devices. At the meeting, however, in direct contravention of the instructions from his superiors, a VW employee, in answering a direct question from CARB, revealed that VW had been using software in its 2.0-liter diesel vehicles to cheat U.S. emissions tests.